EP4092136B8 - Erfassungssonden und verwendungen davon - Google Patents

Erfassungssonden und verwendungen davon Download PDF

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Publication number
EP4092136B8
EP4092136B8 EP21175123.5A EP21175123A EP4092136B8 EP 4092136 B8 EP4092136 B8 EP 4092136B8 EP 21175123 A EP21175123 A EP 21175123A EP 4092136 B8 EP4092136 B8 EP 4092136B8
Authority
EP
European Patent Office
Prior art keywords
capture probes
probes
capture
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Active
Application number
EP21175123.5A
Other languages
English (en)
French (fr)
Other versions
EP4092136C0 (de
EP4092136B1 (de
EP4092136A1 (de
Inventor
Gabriela Ecco
Xiaobin Xing
Adrian Willig
Zhenyu Xu
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Sophia Genetics SA
Original Assignee
Sophia Genetics SA
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Sophia Genetics SA filed Critical Sophia Genetics SA
Priority to EP21175123.5A priority Critical patent/EP4092136B8/de
Priority to EP24156139.8A priority patent/EP4400599A3/de
Priority to US17/484,928 priority patent/US12247255B2/en
Priority to AU2022203042A priority patent/AU2022203042A1/en
Priority to CA3158680A priority patent/CA3158680A1/en
Priority to BR102022009653-8A priority patent/BR102022009653A2/pt
Priority to JP2022082469A priority patent/JP2022179442A/ja
Priority to KR1020220061908A priority patent/KR20220157325A/ko
Publication of EP4092136A1 publication Critical patent/EP4092136A1/de
Application granted granted Critical
Publication of EP4092136C0 publication Critical patent/EP4092136C0/de
Publication of EP4092136B1 publication Critical patent/EP4092136B1/de
Publication of EP4092136B8 publication Critical patent/EP4092136B8/de
Priority to US18/807,281 priority patent/US20250129433A1/en
Active legal-status Critical Current
Anticipated expiration legal-status Critical

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Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869—Methods for sequencing
    • C12Q1/6874—Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1068—Template (nucleic acid) mediated chemical library synthesis, e.g. chemical and enzymatical DNA-templated organic molecule synthesis, libraries prepared by non ribosomal polypeptide synthesis [NRPS], DNA/RNA-polymerase mediated polypeptide synthesis
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • C12Q1/6837—Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6853—Nucleic acid amplification reactions using modified primers or templates
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2549/00—Reactions characterised by the features used to influence the efficiency or specificity
    • C12Q2549/10—Reactions characterised by the features used to influence the efficiency or specificity the purpose being that of reducing false positive or false negative signals
    • C12Q2549/113—Reactions characterised by the features used to influence the efficiency or specificity the purpose being that of reducing false positive or false negative signals using nested probes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Health & Medical Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Engineering & Computer Science (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Genetics & Genomics (AREA)
  • Analytical Chemistry (AREA)
  • Biotechnology (AREA)
  • General Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Immunology (AREA)
  • Molecular Biology (AREA)
  • Biochemistry (AREA)
  • Physics & Mathematics (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Microbiology (AREA)
  • Pathology (AREA)
  • Biomedical Technology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Hospice & Palliative Care (AREA)
  • Oncology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Plant Pathology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
EP21175123.5A 2021-05-20 2021-05-20 Erfassungssonden und verwendungen davon Active EP4092136B8 (de)

Priority Applications (9)

Application Number Priority Date Filing Date Title
EP21175123.5A EP4092136B8 (de) 2021-05-20 2021-05-20 Erfassungssonden und verwendungen davon
EP24156139.8A EP4400599A3 (de) 2021-05-20 2021-05-20 Einfangsonden und verwendungen davon
US17/484,928 US12247255B2 (en) 2021-05-20 2021-09-24 Capture probes and uses thereof
AU2022203042A AU2022203042A1 (en) 2021-05-20 2022-05-06 Capture probes and uses thereof
CA3158680A CA3158680A1 (en) 2021-05-20 2022-05-11 Capture probes and uses thereof
BR102022009653-8A BR102022009653A2 (pt) 2021-05-20 2022-05-18 Conjunto de sondas, sonda, kit, composição, métodos para detecção de um gene de fusão e/ou salto de éxon em uma amostra e para diagnóstico ou monitoramento de um câncer, e, uso de um conjunto de sondas ou de pelo menos uma sonda
JP2022082469A JP2022179442A (ja) 2021-05-20 2022-05-19 捕捉プローブおよびその使用
KR1020220061908A KR20220157325A (ko) 2021-05-20 2022-05-20 캡쳐 프로브 및 이의 용도
US18/807,281 US20250129433A1 (en) 2021-05-20 2024-08-16 Capture probes and uses thereof

Applications Claiming Priority (1)

Application Number Priority Date Filing Date Title
EP21175123.5A EP4092136B8 (de) 2021-05-20 2021-05-20 Erfassungssonden und verwendungen davon

Related Child Applications (2)

Application Number Title Priority Date Filing Date
EP24156139.8A Division-Into EP4400599A3 (de) 2021-05-20 2021-05-20 Einfangsonden und verwendungen davon
EP24156139.8A Division EP4400599A3 (de) 2021-05-20 2021-05-20 Einfangsonden und verwendungen davon

Publications (4)

Publication Number Publication Date
EP4092136A1 EP4092136A1 (de) 2022-11-23
EP4092136C0 EP4092136C0 (de) 2024-02-07
EP4092136B1 EP4092136B1 (de) 2024-02-07
EP4092136B8 true EP4092136B8 (de) 2024-03-13

Family

ID=76059653

Family Applications (2)

Application Number Title Priority Date Filing Date
EP24156139.8A Withdrawn EP4400599A3 (de) 2021-05-20 2021-05-20 Einfangsonden und verwendungen davon
EP21175123.5A Active EP4092136B8 (de) 2021-05-20 2021-05-20 Erfassungssonden und verwendungen davon

Family Applications Before (1)

Application Number Title Priority Date Filing Date
EP24156139.8A Withdrawn EP4400599A3 (de) 2021-05-20 2021-05-20 Einfangsonden und verwendungen davon

Country Status (7)

Country Link
US (1) US12247255B2 (de)
EP (2) EP4400599A3 (de)
JP (1) JP2022179442A (de)
KR (1) KR20220157325A (de)
AU (1) AU2022203042A1 (de)
BR (1) BR102022009653A2 (de)
CA (1) CA3158680A1 (de)

Families Citing this family (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2023056328A2 (en) * 2021-09-30 2023-04-06 Illumina, Inc. Solid supports and methods for depleting and/or enriching library fragments prepared from biosamples

Family Cites Families (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7306916B2 (en) * 2004-05-04 2007-12-11 Dako Denmark A/S Methods for detecting chromosome aberrations
ES2578370T3 (es) * 2011-07-01 2016-07-26 HTG Molecular Diagnostics, Inc Métodos para detectar fusiones génicas
US20150322498A1 (en) * 2012-08-09 2015-11-12 Japanese Foundation For Cancer Research Method for labelling of cleavage of nucleic acid sequence
WO2015026873A1 (en) * 2013-08-19 2015-02-26 Singular Bio, Inc. Assays for single molecule detection and use thereof
EP3647420B1 (de) 2017-06-27 2023-08-23 The University Of Tokyo Sonde und verfahren zum nachweis des transkripts, der aus fusionsgen- und/oder exon-skipping resultiert
CN111321202A (zh) * 2019-12-31 2020-06-23 广州金域医学检验集团股份有限公司 基因融合变异文库构建方法、检测方法、装置、设备及存储介质

Also Published As

Publication number Publication date
EP4092136C0 (de) 2024-02-07
KR20220157325A (ko) 2022-11-29
CA3158680A1 (en) 2022-11-20
EP4400599A2 (de) 2024-07-17
US20220380843A1 (en) 2022-12-01
US12247255B2 (en) 2025-03-11
JP2022179442A (ja) 2022-12-02
BR102022009653A2 (pt) 2022-11-29
EP4092136B1 (de) 2024-02-07
AU2022203042A1 (en) 2022-12-08
EP4092136A1 (de) 2022-11-23
EP4400599A3 (de) 2024-08-28

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